[gmx-users] pdb2gmx and virtual sites

[Justin A. Lemkul]

Ondrej Marsalek wrote:
> I thought that this was needed to convert the hydrogens to virtual
> sites, based on reading section 6.5 of the manual and some other
> things. Is this not correct?
> 

I don't believe constraining angles is necessary.  The manual only refers to 
fixed bond lengths.  If you're looking for an example to follow, I would suggest 
running the lysozyme benchmark described in the GROMACS 4 paper; the parameters 
used are nicely detailed.  I got reasonable results using "constraints = 
all-bonds," but if that is not correct, perhaps someone else can comment.

-Justin

> Ondrej
> 
> 
> On Wed, Nov 4, 2009 at 20:07, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>>
>> Ondrej Marsalek wrote:
>>> Dear GROMACS users,
>>>
>>> I would like to substitute hydrogens in a protein with virtual sites
>>> to allow for the 4-5 fs timestep mentioned in the GROMACS 4 paper and
>>> several other places. So far, I have not found an example or a
>>> tutorial that would involve this, so I want to create a
>>> straightforward example. I have taken the 2KO3 structure from the PDB
>>> and went through this sequence of commands:
>>>
>>> pdb2gmx -v -f 2KO3.pdb -o initial-vacuum.gro -ff oplsaa -water tip4p
>>> -vsite hydrogens -ignh
>>> editconf -f initial-vacuum.gro -o initial-box.gro -c -d 1 -bt cubic
>>> genbox -cp initial-box.gro -cs tip4p.gro -p topol.top -o conf.gro
>>> grompp
>>>
>>> I also provided a pretty standard grompp.mdp, that contains
>>> "constraints = h-angles". I get the following error:
>>>
>>> -------------------------------------------------------
>>> Program grompp, VERSION 4.0.5
>>> Source code file: vsite_parm.c, line: 779
>>>
>>> Fatal error:
>>> Automatic parameter generation not supported for Virtual site 3 atom 4
>>> for this bonding configuration
>>> -------------------------------------------------------
>>>
>>> I am not sure what the problem is. I would appreciate and help on the
>>> use of this feature, pointers to resources, or a working example.
>>> Reading the manual and searching did not help as much as I would like.
>>>
>> Have you tried specifying either "all-bonds" or "h-bonds" for constraints?
>>  I think "all-bonds" is the most commonly-used option.  Any specific reason
>> for using "h-angles"?
>>
>> -Justin
>>
>>> Thanks,
>>> Ondrej
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>> --
>> ========================================
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> ========================================
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> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================